Full disclosure: There are so many good series on TV right now that it's all but impossible to keep up with all of them. That sentiment might run counter to a lot of the complaints you see in this space, and while those complaints are true (e.g., Two and a Half Men is far too popular), they tend to dilute the fact that we're living in a great age for television. This is especially true when you consider cable offerings, which make it easier to see cutting-edge dramas and comedies that the networks avoid.
All that said: There's no way this list will remotely due justice to all the good shows out there. Your favorite show might not be on the list. I ask only a little leniency as you remember that coming up with the best five episodes was like choosing between children, only tougher, because kids don't respond to the TiVo remote. Trust me: tough calls were made.
Let's do this!